LOC108214418

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108214418
Identifier: 
LOC108214418
Cross Reference: 
NCBI Gene
Relationship: 
There are 5 relationships.
Relationships
The mRNA, XM_017386406.1, is a part of gene, LOC108214418.
The genetic_marker, MK002799 K0243, is located in gene, LOC108214418.
The genetic_marker, MK002192 ESSR-087, is located in gene, LOC108214418.
The genetic_marker, MK002294 ESSR-189, is located in gene, LOC108214418.
The genetic_marker, MK017380 3_2089305, is located in gene, LOC108214418.
Analysis: 
NameDescription
Carrot Genome Assembly DCARv2

An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4.

There are a few different naming schemes for this assembly. First there is the
Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.

Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0

LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926.

Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence.

RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records.

The NCBI Sequence report lists the correspondences between the various naming methods

Link to the LNRQ01000000.1 master record at NCBI

Raw Reads: Link to SRA accessions used for the genome assembly

This genome is available in the CarrotOmics Blast Search
NCBI Daucus carota subsp. sativus Annotation Release 100

The RefSeq genome records for Daucus carota subsp. sativus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

View the full report at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Daucus_carota_subsp._sativus/100/

Data from this analysis can be viewed in JBrowse here.
Transcripts: 
Transcript NameIdentifierTypeLocation
XM_017386406.1XM_017386406.1mRNADCARv2_Chr3:2083026..2090273
Sequence: 
AGGTATATAAACACGATCTAACAAAACAGTAGTTTCACTAGACAGAACAT
CAACTCAACTCATCTCTCTCTCTCTCTAAGGTCACCATTATTCTCTCTCT
CTCTCTCTCTCTCACCTCCCCTCCTCCCCCTCTCTCTCGCCTCCAATTCT
CTCTCTCTCTCTCTCTCTCTCTATCTCTCACCTCCCCTCCTCCCCCTCTC
TCTCGCCTCCAATTCTCTCTCTCGCCTCCAATTCTCTCTCTCTCTCTCTC
TCTCTCTATCTCTCTCTCTAATTGTTAGAAATTTTAAATAGATTAATTAA
TTATTTAATTTCTGCTGATTATAATTGGTTTTGGTGGATAATCTGCTTTA
GGATTTTTAGAAGGATTCAATTATTGATAATGACGGTGTTAATTAATTAA
TAATTGTAGGGTTGAGTTTGTTCGGGGAGAAATTTTTGGGGGCTTTAATT
ATAGAATATTCTGTTTAGGGGAGGTACTTTTAATTTTAAATTGTAGTGTT
ATTTGTTCAAGGTGAAGTATATTCTATCTGTTTTTTTGCTTAATTTTTTG
ATCATGTATGTTTTTTGAATTATAATGTAAAGATGTTTTTAGTGTAAATT
AGGGTTTGTTGTAGGAGAAATTTAGGGGTTTTGGTTTGTGAGTAGATTAA
ATGTTTGTAATAGAGGGGTGTTACTCCTTAGGATTATGACAAAAGGGGTT
TCTTGGATTTTTGTTTTGAAATTTCGGGACTTTAATATCGCTGATAATTT
GTAGTTAGTTCAAGAAATGGTTCTCATTGTCATGATTTGATCTGCATTTG
CATTCCGTGTGTTGATTAGATTAGATGCTTGTAAAAGTAAAACCAAATAT
GCTTTGAGCGTCTCTTTGCTCTGATGTGCTTCTATGTGTTTATGCGGTCA
GACTCTAGTCAATTGCTTCAGTTAATCTGTGAAGTAATCTTTTGTTTGTT
TATTTTCTTTTTAGTTCAAATTGCAAAGGCAAAGGGCTTGAACTACCAAA
AAAGCGCTATTCTTGCCCTTATTGTACAGATTGACCATCTGGATTCAGAA
CCTAAATCTATGTGGGGAATTGTAAGAGGGTAATACTTCGAGTGGATACT
AGCTCTCTCTGAATTTCAAAGCTGAAAGGAGAGGAACTGGATACCTACTT
GGATAATAGCCACCAGGCAGCAGGGCAGACAATGGCGCCTTCCCGGGTGG
CTGGTGGATTAGCAGGATTGGCTAATTCTTCTACGAATTCTGGAATCTTT
TTCCAAGGTGATAGGCAGTCTCATGTTGTTGGAAACTCACACTTGAGTTC
TTTTGGAAACTCTATTAATTCAAATTCTGGAAACCTGCGTTCTAACATGG
GGCCAAATTCCGGGGATGTAAGTAATACATTATTAAACAGTGTGGCTGCC
TCTGGGCCTAGTGTTGGAGCAAGCTCATTGGTTACTGATGCAAACTCGGG
ACTTTCTGTTGGCCCAAATCTTCAGAGGAGTGCTAGCTTTAATACAGACT
CGTACATGCGGTTACCAGCTTCACCCATGTCATTCTCGTCCAATAACATA
AGCATTTCAGCTTCATCAGTCCTGGACGGGTCTTCTGTTGTGCAGCAGAA
CTCTAACAAAGACCCTAATTGCTATCAGAGTCAACAACACCAAGGGACAT
CTAGTGCCACATCATTTTCAGCTGGGCGAGCGGGGCAAATATCACTTCCT
TCTGGCCCAAGAATTCCTGGATCTTTCATTCAAGATCCCCTCTCGCACTT
GCAGAAGAAGCCTCGATTGGATATTAAACAGGAAGACATCCAGCAACAAC
AGGCTATACAACAGATTCTACAAAGACAAGATCCTATGCAGATACAAAAC
CCTAATCCTCAGTTGCAAGCTTTAATACAGCAACAGCGACTTAGGCAACA
GCAGCAGCAACAGCAACAACTACTGCAGTCTATGCCACAAATGCAGCGAG
CTCAGTTGCTGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCTGCAGATG
AGACAGCAGCTTCAACAGGGGGTGCAGCCTGCTTCTGCTGGAAAGCGACC
TTATGATGGTGGCGTTTGTTCTCGTCGACTGATGCAGTATCTATATCATC
AGAGGCAGCGACCACAAGTGAGTATTTCTTTTGGAGCACCCATGTTTAGT
TTTGATACATAAACCCTCAGTTTTGAATCTATGATAATTTCTTCATCCTT
GTCAGTCTTTACCCTGTATCTGTTATGTTACTTATGTTGGGTTTCAATTT
TTTAATTGTAATCACATCTCATATTATGAACAGGACAATACTTTTACCTA
CTGGAGGAAATTTGTGGCGGAGTACTATTCTCCACGGGCAAAGAAAAGAT
GGTGCTTGTCATTATATGATAATGTTGGGATTCACTCTCTTGGTGTATTT
CCTCAGGCGGCCATGGTTAGCTATATCTTTAAATTTTGTACTTCTGCAAA
TGGGGCATAAAATATAGTACTGTTTTAATCTATTAGCTATAATGTAATTG
AAGTATTGAACTAATGAGCAAATACCAAAATAACTTCCAAGTATAGATGA
AGAATAATAATGTAAGATCCTATAATTTCTTTGTTTTGTGTTGTTTGATT
TAAAAAATTTCAGCATTGCATCTCACTAAATGATCTTTTCTTTCTGCTTG
CAAGGATGCTTGGCAGTGCGATATTTGTGGTTCGAAATCAGGAAGGGGAT
TTGGTGAGTGTTACTTGGTAGTAGGATATCATAATTATAAATGTTTGTAC
TCAAAAGTTGTTGGAGGTTAAGGGTGTAGCTTACTTTGGATTTTAAATAG
CTTTTCGTCACTTACCTTTTTTCATTGGATGACCCTTGGACCCTTGCCTT
TGCCATATAGACCTTATGTTTATCTACATCTTTTGTTTAGCTCCTTCTGT
TATTTCTCTGCTGAGCGTGGGTGGCATAGCCACTCTTTTTGATAAAGATG
TACATTTTTTTCTATTTTAATTGATAATGTCTTCTTATTACATATATGAC
ATATGTTTAGGTAAAAGAATGGTTTCAACTATTTTATACGTGTCTTGCTT
TCCATCGATTGGTTAAATAGTAGGACATCTTGTCAGATCTTTAGACTAGC
TTAGGCATATTTTGAATTTCCCCTGTTTTTGCAGTTACTTTATCAAGATG
TGGGCTGTAAAGGGTGTTAGTTGGCAATTGCATAAGATTAATATTCAGTC
AAATATTCTGACTTTTTACTGTTGATTTCGATTTCAACAGAGGCAACTTT
TGAAGTACTCCCTCGACTAAATGAGATTAAATTTGGTAGCGGAGTCATTG
ATGAGCTTTTGTATCTTGACTTACCACGTGAATGTAGACTTTCTTCCGGA
GTAATGATGTTGGAATATGGAAAAGCAGTTCAGGAAAGTGTTTATGAGCA
ACTGAGGGTGGTTCGTGAGGGCCAGCTCCGTGTCATATTCACCCCAGACC
TAAAGGTCTATATTTTTTCTCATTTTGATTGCTGTACAGTTGTAATCTTC
TTCCTGAACCTTTTACACATGTTTCAGATATTATCTTGGGAATTTTGTGC
AAGGCACCATGAAGAACTTCTTCCCCGTAGGTTGGTTGCACCACAGGTTA
GGCATATCTTTAAAAAGTAAATGTTCCAATTCACTTTTCTATATACTCTT
TAAAAACTTGCTTCCAATTGTATGGCATTCGGTCAAAGATTATATTGTGC
CTATGTCCGCATCAAGATTTTTTATTTTTAGAAGAATTTCCATTGCTTCT
ACTTGTGTTTTAGGTTCTCAAAAGTATACATTGCAAACAATCTCTTTAAA
CATAGAACTAATAGAGAGATGGGAGGCAGATGAATAGAGTATAATGATTT
AAGTTTAGTTTCTTACATACACCTGTGACCTATCAGGCTGTCATATTTCA
TATTTACAAGTTTTCCTTTTTGTATTGTATTCATAGCATAGTTTGATGTT
TAGGATCTGTCATTTTTATCAGCTATATGTGTTGGCTGTTAGCCTATTTA
GTCATATGACCATTTGTAGGATTATATTGATAATTTGAACTCTGTTCAGA
AATTTTACAGTTGATTGAAGGTTTAAAATTCCTTTCAGGTGAATCAGTTG
TTACAGGTTGCACAGAAATGCCAAAGCACTATTACTGAAAGTGGGTCAGA
TGGGGTCTCTCAGCAGGATTCGCAGAATACTAGTAATATGTGAGTTGCAT
TTTATGTTTTCATGTCTATGGGTAATCTGATGTGAAATGGGGCTATACTT
ATCTGCATCAATACACCTTTGCAATTGACATCTGATATTTGATATTAGTA
ATGAGTATTTAGGTAGTGCATGTGGCCTGCTTTGTATCCACTACTATATG
ATTCCAGGTCTGGTCTCTATTTCGAGGGGAAAACATAGAGATACATGATC
AGTGACCTTACATCCCTATGTAATATTATCTATATTTTTTGGTAGTCAAT
TATGATTTTTTTTTTTGCTACATAATTAATTCTGATCTTTTTTAGTTGTC
TGGATGCAATTTAGTTGGTTGATATTTTTATGTGTGAATCCAGAGCTTAA
TGTTTAATTATTTTGTCCAAATGGCTGTGTTGCTTACAATTGACAATGTG
TCAGGATGGTGACAGCTGCCCGCCAATTTGCTAAGAGTCTAGAGTCGCAG
TCTTTGAATGACTTGGGATTTTCCAAAAGATATGTGCGATGCTTACAGGT
AGCTTTTTTTGGTGTATTCAAGTAAGAGTGTGGGGTATGGTTAAATTCTT
GTGATGTTTATGATATCAAGTTAAACAACTTTTAAACAGATATCGGAGGT
TGTCAACAGCATGAAGGATCTTATGGATTTCTGCAGAGACCAGAAAGATG
GACCAATGGGTAAGTACTATTCATGTAGTTTCTAGCATTAATTCAATCTA
GTTATAAGTACAAACGTTAGGGGTTCAAATGTCACCTGTGTTTAGTTTTA
AGTACAATTAAACACATCTGAGTTGTATTTTTCTCTGATAAAATACACAT
AAATATTTTTTCCCACTCAATGTTGTATTCTAGAAGTGGCAGTATGGTGG
ACCGTGTTCCTGTTAAAATTGAATATATCTACAAATAAATACTTCCCCAA
GAACTGGCATTGTTGTCTTATTATTATCTTAATTATCCAATTACAGTCAT
GTACCAAACAAAGGATAGATATAGCTAATATAAGTATGTGAAATTCTTGA
ACTAGGAAATAGGAAACTTTGAGGATTGCATTTTAATATGTATATTTATA
TTTTTATTTCTAGTCAAAAGTATTCCAGGTTTAGAACATGGGTTATCTTC
CGTACCTCTTTAGAGTTTGGAAATTTGCCCATAATCATTGCATTTATTAG
AATAAGTTGAGATATTAGCTTCGTTCGTCCCGATAGCTGATTTGGAAAGG
AGCTTCTACCTTTGTTTCGGAGCCGTTCTGCAGGGTTGATACTTGACAGC
CCTTGATCTGAGTTTTTCTTGTTCCTATTTACTTGATAACATAATAACAT
ATTGGTTGACCAGGCCAGAACTGAATTCCAATTTTCTTGTAGTATAATGC
TTATATTAGTAATTTGTAAATTTGATTTTATTAAATAGAAACTGGTCCCC
CTATTTAAACACTTCTCCTGCTACTACTGTCTTGCAGAGAGTTTAAAGAA
ATTCCCTCGACTTGCCAGTCCTGCCAAGTTTCAGCTTCAGAAGATGCAGG
AGTTGGAACAGATGGCCAGTATTAATGGTTTGCAAACTGATCGTGGAACA
CTCAACAAGCTAGTAGCACAAAATGGGGGGCTTAATAATCAGATCAATTG
TAACAATCAAATGGTTGGGCGAGCAGCCTTAAGTGGGTCGCCTCAAGCTG
CCATGGCCCTTTCAAACTATCAGAATATGCTGATGAGACAAAACTCTTTT
AATTCTAATTCTAATTCAGCTCAACAGGAGGCAACTTCCTCTGTGAGCAA
TGTGAACCAGAAAGCATCCCCGTCTTTCCAAGGGTCTGCTTCTGTATTGT
CAGGGACAATGCAGAATCCACAGACCAGTGGATTCTCAAGTTCCCATTTC
TTGCAATCGCATCAACGTGCTCTTAATGTTAACGGTGGTCTGCAACAGAA
CCATCTGCAATCTCCTCAAAACAGCCAGGGCTTGCAACAACAAATGATCC
AGCGGCTGCTACAAGATATAAATAGTAACAACAATACAGGGGGTGTACAA
CCACAGCAGCAGCCCCTTGCTGGAAACAGTGCTAATGTTAGTGCGGGAAG
TGATGGTCTTGGGTATGGGAGCAACACGTCTATGGGATCAGCAGCTCAGG
TGAATAGAGTAGCTACTACAAACAATCCAATGCCAACCAGGAGCAATAGT
TTCAAAGGAGTTTCAGCTAGTGATTCTTCTGCAGCTGTTGGCAATAATGG
GAACAGCCAGAGAGCATGTGATATACCACAAAATCTTCAGTTGTCAGACG
AATTGGCACAGGATATTGCTCAGGAATTTTCAGAACATGGTCTTTTTAGT
GATCTTGAGGAAAGTATGGCATATGGTGGCTGGAAGACAGGATTGTAACT
CACGTGAACGGCTTCTGTTGGGTCAGTTTCTCTATGTACATGTTTAATTA
TATTAGGTCATGTGTTTCCCGTCCTATTGAAGCCGAACACACATAAACTC
GTTACAGTACGAAAAAGTTAGGAAATGTTTAGAGTGTTTAGTTCCCCCTC
TTTTTCTCGTTTATGGTACCAAACCCATCCAACTGTAATTTTTTTGGTAA
ATGGCGATTACAAGAAACTTTGTATACTCAGGCCTGCATGTTTGCACTAA
CATCCAGCTTGAAATACCCTGTCCATCTGTAATATTTGAGGACAAATCCC
TATTGTGGTACCAATACATTTTCATGCATCTGTGATCAGCTTGTTCATTG
CTCCGAGTTGCTGGCGTGACCTGCTCGTATCGGAAGTTTGATAGTATATT
AACCTGTGTTTTTGACCGTGTGTGATGTCACTAGCTGTCATTAGCGAGAA
ACCAAGACAAATTTGAAGCGAGAGAAGCCAGAGAATTCTATGAAACTGTT
AGTGCAGACTGCAGAAGAGACTGGCTGAGAATCTGTATTTATGTTTCTGC
TGTATTAACAGTTTTAGGAATCTCATTGTGTCTGGCAGAGTAATAAAGAC
GTTTACCCATTTATATATTTTTCTTATGATAGAAGAATGTTTATACCTAA
AATATGTAATATTATGGTAGTATACAATCGAAAGAATGTTTTGTTTA
Sequence Length: 
7247
Sequence Checksum: 
976f614c60323317e08c24c1c3e00af1
View location in JBrowse: 
DCARv2_Chr3:2083027..2090273+
Gene: 
LOC108214418
Gene Biotype: 
protein_coding
Gbkey: 
Gene